[package - head-armv6-default][biology/cufflinks] Failed for cufflinks-2.2.1.89_1 in build
pkg-fallout at FreeBSD.org
pkg-fallout at FreeBSD.org
Thu Aug 27 01:27:52 UTC 2020
You are receiving this mail as a port that you maintain
is failing to build on the FreeBSD package build server.
Please investigate the failure and submit a PR to fix
build.
Maintainer: yuri at FreeBSD.org
Last committer: jwb at FreeBSD.org
Ident: $FreeBSD: head/biology/cufflinks/Makefile 544090 2020-08-03 17:40:04Z jwb $
Log URL: http://beefy8.nyi.freebsd.org/data/head-armv6-default/p546132_s364744/logs/cufflinks-2.2.1.89_1.log
Build URL: http://beefy8.nyi.freebsd.org/build.html?mastername=head-armv6-default&build=p546132_s364744
Log:
=>> Building biology/cufflinks
build started at Thu Aug 27 01:16:14 UTC 2020
port directory: /usr/ports/biology/cufflinks
package name: cufflinks-2.2.1.89_1
building for: FreeBSD head-armv6-default-job-06 13.0-CURRENT FreeBSD 13.0-CURRENT 1300111 arm
maintained by: yuri at FreeBSD.org
Makefile ident: $FreeBSD: head/biology/cufflinks/Makefile 544090 2020-08-03 17:40:04Z jwb $
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!!! Jail is newer than host. (Jail: 1300111, Host: 1300100) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
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=======================<phase: check-sanity >============================
===> License BSL accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> cufflinks-2.2.1.89_1 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.14.7.txz
[head-armv6-default-job-06] Installing pkg-1.14.7...
[head-armv6-default-job-06] Extracting pkg-1.14.7: .......... done
===> cufflinks-2.2.1.89_1 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of cufflinks-2.2.1.89_1
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License BSL accepted by the user
===> Fetching all distfiles required by cufflinks-2.2.1.89_1 for building
===========================================================================
=======================<phase: checksum >============================
===> License BSL accepted by the user
===> Fetching all distfiles required by cufflinks-2.2.1.89_1 for building
=> SHA256 Checksum OK for cole-trapnell-lab-cufflinks-v2.2.1-89-gdc3b0cb_GH0.tar.gz.
<snip>
{ if (lf.mi!=NULL) lf.mi[MEV] = ENULL;
~~~^~ ~~~~
2 warnings generated.
mv -f .deps/startlf.Tpo .deps/startlf.Po
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -MT strings.o -MD -MP -MF .deps/strings.Tpo -c -o strings.o `test -f 'locfit/strings.c' || echo './'`locfit/strings.c
mv -f .deps/strings.Tpo .deps/strings.Po
/nxb-bin/usr/bin/c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++03 -pthread -I/usr/local/include -I/usr/local/include -I/usr/local/include/eigen3 -MT vari.o -MD -MP -MF .deps/vari.Tpo -c -o vari.o `test -f 'locfit/vari.cpp' || echo './'`locfit/vari.cpp
mv -f .deps/vari.Tpo .deps/vari.Po
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -MT wdiag.o -MD -MP -MF .deps/wdiag.Tpo -c -o wdiag.o `test -f 'locfit/wdiag.c' || echo './'`locfit/wdiag.c
mv -f .deps/wdiag.Tpo .deps/wdiag.Po
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -MT weight.o -MD -MP -MF .deps/weight.Tpo -c -o weight.o `test -f 'locfit/weight.c' || echo './'`locfit/weight.c
mv -f .deps/weight.Tpo .deps/weight.Po
/nxb-bin/usr/bin/c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++03 -pthread -I/usr/local/include -I/usr/local/include -I/usr/local/include/eigen3 -MT replicates.o -MD -MP -MF .deps/replicates.Tpo -c -o replicates.o replicates.cpp
In file included from replicates.cpp:12:
./locfit/local.h:126:9: warning: 'MAX' macro redefined [-Wmacro-redefined]
#define MAX(a,b) (((a)>(b)) ? (a) : (b))
^
/usr/include/sys/param.h:311:9: note: previous definition is here
#define MAX(a,b) (((a)>(b))?(a):(b))
^
In file included from replicates.cpp:12:
./locfit/local.h:127:9: warning: 'MIN' macro redefined [-Wmacro-redefined]
#define MIN(a,b) (((a)<(b)) ? (a) : (b))
^
/usr/include/sys/param.h:310:9: note: previous definition is here
#define MIN(a,b) (((a)<(b))?(a):(b))
^
In file included from replicates.cpp:18:
In file included from ./replicates.h:10:
In file included from ./bundles.h:22:
./hits.h:906:48: warning: field '_expression_file_name' will be initialized after field '_ifs' [-Wreorder-ctor]
HitFactory(insert_table, reference_table), _expression_file_name(expression_file_name), _ifs(expression_file_name.c_str()),
^
In file included from replicates.cpp:18:
./replicates.h:224:57: warning: unused variable 's2' [-Wunused-variable]
const vector<boost::shared_ptr<Scaffold> >& s2 = bundles[i-1]->ref_scaffolds();
^
In file included from replicates.cpp:18:
In file included from ./replicates.h:10:
In file included from ./bundles.h:16:
In file included from /usr/local/include/boost/random.hpp:36:
In file included from /usr/local/include/boost/random/additive_combine.hpp:27:
/usr/local/include/boost/random/linear_congruential.hpp:140:20: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare]
if(_x <= 0 && _x != 0) {
~~~~~~~~^~~~~~~~~~
/usr/local/include/boost/random/linear_congruential.hpp:393:11: note: in instantiation of member function 'boost::random::linear_congruential_engine<unsigned long long, 25214903917, 11, 281474976710656>::seed' requested here
{ lcf.seed(cnv(x0)); }
^
In file included from replicates.cpp:9:
In file included from /usr/local/include/boost/thread.hpp:13:
In file included from /usr/local/include/boost/thread/thread.hpp:12:
In file included from /usr/local/include/boost/thread/thread_only.hpp:17:
In file included from /usr/local/include/boost/thread/pthread/thread_data.hpp:12:
In file included from /usr/local/include/boost/thread/lock_types.hpp:18:
In file included from /usr/local/include/boost/thread/thread_time.hpp:9:
In file included from /usr/local/include/boost/date_time/time_clock.hpp:17:
In file included from /usr/local/include/boost/shared_ptr.hpp:17:
In file included from /usr/local/include/boost/smart_ptr/shared_ptr.hpp:26:
In file included from /usr/local/include/boost/checked_delete.hpp:15:
/usr/local/include/boost/core/checked_delete.hpp:36:5: warning: delete called on non-final 'PoissonDispersionModel' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor]
delete x;
^
/usr/local/include/boost/smart_ptr/detail/shared_count.hpp:149:20: note: in instantiation of function template specialization 'boost::checked_delete<PoissonDispersionModel>' requested here
boost::checked_delete( p );
^
/usr/local/include/boost/smart_ptr/shared_ptr.hpp:285:5: note: in instantiation of function template specialization 'boost::detail::shared_count::shared_count<PoissonDispersionModel>' requested here
boost::detail::shared_count( p ).swap( pn );
^
/usr/local/include/boost/smart_ptr/shared_ptr.hpp:379:24: note: in instantiation of function template specialization 'boost::detail::sp_pointer_construct<MassDispersionModel, PoissonDispersionModel>' requested here
boost::detail::sp_pointer_construct( this, p, pn );
^
replicates.cpp:793:21: note: in instantiation of function template specialization 'boost::shared_ptr<MassDispersionModel>::shared_ptr<PoissonDispersionModel>' requested here
disperser = boost::shared_ptr<MassDispersionModel>(new PoissonDispersionModel(condition_name));
^
In file included from replicates.cpp:9:
In file included from /usr/local/include/boost/thread.hpp:13:
In file included from /usr/local/include/boost/thread/thread.hpp:12:
In file included from /usr/local/include/boost/thread/thread_only.hpp:17:
In file included from /usr/local/include/boost/thread/pthread/thread_data.hpp:12:
In file included from /usr/local/include/boost/thread/lock_types.hpp:18:
In file included from /usr/local/include/boost/thread/thread_time.hpp:9:
In file included from /usr/local/include/boost/date_time/time_clock.hpp:17:
In file included from /usr/local/include/boost/shared_ptr.hpp:17:
In file included from /usr/local/include/boost/smart_ptr/shared_ptr.hpp:26:
In file included from /usr/local/include/boost/checked_delete.hpp:15:
/usr/local/include/boost/core/checked_delete.hpp:36:5: warning: delete called on non-final 'MassDispersionModel' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor]
delete x;
^
/usr/local/include/boost/smart_ptr/detail/shared_count.hpp:149:20: note: in instantiation of function template specialization 'boost::checked_delete<MassDispersionModel>' requested here
boost::checked_delete( p );
^
/usr/local/include/boost/smart_ptr/shared_ptr.hpp:285:5: note: in instantiation of function template specialization 'boost::detail::shared_count::shared_count<MassDispersionModel>' requested here
boost::detail::shared_count( p ).swap( pn );
^
/usr/local/include/boost/smart_ptr/shared_ptr.hpp:379:24: note: in instantiation of function template specialization 'boost::detail::sp_pointer_construct<MassDispersionModel, MassDispersionModel>' requested here
boost::detail::sp_pointer_construct( this, p, pn );
^
replicates.cpp:871:17: note: in instantiation of function template specialization 'boost::shared_ptr<MassDispersionModel>::shared_ptr<MassDispersionModel>' requested here
disperser = boost::shared_ptr<MassDispersionModel>(new MassDispersionModel(condition_name, compatible_count_means, raw_variances, fitted_values));
^
7 warnings generated.
mv -f .deps/replicates.Tpo .deps/replicates.Po
/nxb-bin/usr/bin/c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++03 -pthread -I/usr/local/include -I/usr/local/include -I/usr/local/include/eigen3 -MT multireads.o -MD -MP -MF .deps/multireads.Tpo -c -o multireads.o multireads.cpp
In file included from multireads.cpp:11:
./hits.h:906:48: warning: field '_expression_file_name' will be initialized after field '_ifs' [-Wreorder-ctor]
HitFactory(insert_table, reference_table), _expression_file_name(expression_file_name), _ifs(expression_file_name.c_str()),
^
In file included from multireads.cpp:11:
In file included from ./hits.h:32:
./multireads.h:27:11: warning: private field '_id' is not used [-Wunused-private-field]
InsertID _id;
^
2 warnings generated.
mv -f .deps/multireads.Tpo .deps/multireads.Po
/nxb-bin/usr/bin/c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++03 -pthread -I/usr/local/include -I/usr/local/include -I/usr/local/include/eigen3 -MT jensen_shannon.o -MD -MP -MF .deps/jensen_shannon.Tpo -c -o jensen_shannon.o jensen_shannon.cpp
jensen_shannon.cpp:31:2: warning: misleading indentation; statement is not part of the previous 'if' [-Wmisleading-indentation]
return e;
^
jensen_shannon.cpp:29:5: note: previous statement is here
if (e < 0)
^
jensen_shannon.cpp:67:2: warning: misleading indentation; statement is not part of the previous 'if' [-Wmisleading-indentation]
return sqrt(js);
^
jensen_shannon.cpp:65:5: note: previous statement is here
if (js < 0) // can happen due to underflow or rounding errors.
^
jensen_shannon.cpp:132:24: warning: unused variable 'curr_grad' [-Wunused-variable]
double curr_grad = gradient(i*kappa_length + k);
^
3 warnings generated.
mv -f .deps/jensen_shannon.Tpo .deps/jensen_shannon.Po
/nxb-bin/usr/bin/c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++03 -pthread -I/usr/local/include -I/usr/local/include -I/usr/local/include/eigen3 -MT tracking.o -MD -MP -MF .deps/tracking.Tpo -c -o tracking.o tracking.cpp
In file included from tracking.cpp:1:
In file included from ./tracking.h:1:
In file included from ./abundances.h:23:
./hits.h:906:48: warning: field '_expression_file_name' will be initialized after field '_ifs' [-Wreorder-ctor]
HitFactory(insert_table, reference_table), _expression_file_name(expression_file_name), _ifs(expression_file_name.c_str()),
^
In file included from tracking.cpp:1:
In file included from ./tracking.h:1:
In file included from ./abundances.h:25:
In file included from ./bundles.h:16:
In file included from /usr/local/include/boost/random.hpp:36:
In file included from /usr/local/include/boost/random/additive_combine.hpp:27:
/usr/local/include/boost/random/linear_congruential.hpp:140:20: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare]
if(_x <= 0 && _x != 0) {
~~~~~~~~^~~~~~~~~~
/usr/local/include/boost/random/linear_congruential.hpp:393:11: note: in instantiation of member function 'boost::random::linear_congruential_engine<unsigned long long, 25214903917, 11, 281474976710656>::seed' requested here
{ lcf.seed(cnv(x0)); }
^
2 warnings generated.
mv -f .deps/tracking.Tpo .deps/tracking.Po
rm -f libcufflinks.a
ar cru libcufflinks.a clustering.o differential.o common.o assemble.o tokenize.o abundances.o scaffolds.o hits.o genes.o bundles.o filters.o scaffold_graph.o matching_merge.o graph_optimize.o biascorrection.o sampling.o adap.o ar_funs.o arith.o band.o c_args.o c_plot.o cmd.o dens_haz.o dens_int.o dens_odi.o density.o dist.o ev_atree.o ev_interp.o ev_kdtre.o ev_main.o ev_trian.o family.o fitted.o frend.o help.o lf_dercor.o lf_fitfun.o lf_robust.o lf_vari.o lfd.o lfstr.o linalg.o locfit.o m_chol.o m_eigen.o m_jacob.o m_max.o makecmd.o math.o minmax.o nbhd.o pcomp.o pout.o preplot.o random.o readfile.o scb.o scb_cons.o simul.o solve.o startlf.o strings.o vari.o wdiag.o weight.o replicates.o multireads.o jensen_shannon.o tracking.o
ranlib libcufflinks.a
/nxb-bin/usr/bin/c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++03 -pthread -I/usr/local/include -I/usr/local/include -I/usr/local/include/eigen3 -MT codons.o -MD -MP -MF .deps/codons.Tpo -c -o codons.o codons.cpp
mv -f .deps/codons.Tpo .deps/codons.Po
/nxb-bin/usr/bin/c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++03 -pthread -I/usr/local/include -I/usr/local/include -I/usr/local/include/eigen3 -MT GArgs.o -MD -MP -MF .deps/GArgs.Tpo -c -o GArgs.o GArgs.cpp
mv -f .deps/GArgs.Tpo .deps/GArgs.Po
/nxb-bin/usr/bin/c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++03 -pthread -I/usr/local/include -I/usr/local/include -I/usr/local/include/eigen3 -MT GBase.o -MD -MP -MF .deps/GBase.Tpo -c -o GBase.o GBase.cpp
mv -f .deps/GBase.Tpo .deps/GBase.Po
/nxb-bin/usr/bin/c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++03 -pthread -I/usr/local/include -I/usr/local/include -I/usr/local/include/eigen3 -MT gdna.o -MD -MP -MF .deps/gdna.Tpo -c -o gdna.o gdna.cpp
mv -f .deps/gdna.Tpo .deps/gdna.Po
/nxb-bin/usr/bin/c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++03 -pthread -I/usr/local/include -I/usr/local/include -I/usr/local/include/eigen3 -MT GStr.o -MD -MP -MF .deps/GStr.Tpo -c -o GStr.o GStr.cpp
mv -f .deps/GStr.Tpo .deps/GStr.Po
/nxb-bin/usr/bin/c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++03 -pthread -I/usr/local/include -I/usr/local/include -I/usr/local/include/eigen3 -MT GFaSeqGet.o -MD -MP -MF .deps/GFaSeqGet.Tpo -c -o GFaSeqGet.o GFaSeqGet.cpp
mv -f .deps/GFaSeqGet.Tpo .deps/GFaSeqGet.Po
/nxb-bin/usr/bin/c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++03 -pthread -I/usr/local/include -I/usr/local/include -I/usr/local/include/eigen3 -MT GFastaIndex.o -MD -MP -MF .deps/GFastaIndex.Tpo -c -o GFastaIndex.o GFastaIndex.cpp
mv -f .deps/GFastaIndex.Tpo .deps/GFastaIndex.Po
/nxb-bin/usr/bin/c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++03 -pthread -I/usr/local/include -I/usr/local/include -I/usr/local/include/eigen3 -MT gff.o -MD -MP -MF .deps/gff.Tpo -c -o gff.o gff.cpp
gff.cpp:1219:30: warning: result of comparison of constant 'exgffIntron' (-1) with expression of type 'char' is always false [-Wtautological-constant-out-of-range-compare]
if (!(gffline->exontype==exgffIntron && (parentgfo->isTranscript() || parentgfo->exons.Count()>0))) {
~~~~~~~~~~~~~~~~~^ ~~~~~~~~~~~
1 warning generated.
mv -f .deps/gff.Tpo .deps/gff.Po
/nxb-bin/usr/bin/c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++03 -pthread -I/usr/local/include -I/usr/local/include -I/usr/local/include/eigen3 -MT gff_utils.o -MD -MP -MF .deps/gff_utils.Tpo -c -o gff_utils.o gff_utils.cpp
mv -f .deps/gff_utils.Tpo .deps/gff_utils.Po
/nxb-bin/usr/bin/c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++03 -pthread -I/usr/local/include -I/usr/local/include -I/usr/local/include/eigen3 -MT gtf_tracking.o -MD -MP -MF .deps/gtf_tracking.Tpo -c -o gtf_tracking.o gtf_tracking.cpp
mv -f .deps/gtf_tracking.Tpo .deps/gtf_tracking.Po
rm -f libgc.a
ar cru libgc.a codons.o GArgs.o GBase.o gdna.o GStr.o GFaSeqGet.o GFastaIndex.o gff.o gff_utils.o gtf_tracking.o
ranlib libgc.a
/nxb-bin/usr/bin/c++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++03 -pthread -I/usr/local/include -I/usr/local/include -I/usr/local/include/eigen3 -fstack-protector-strong -pthread -L/usr/local/lib -L/usr/local/lib -fstack-protector-strong -o cufflinks cufflinks.o libcufflinks.a libgc.a -lboost_thread -lboost_system -lboost_serialization -lboost_filesystem -lhts -lz
ld: error: duplicate symbol: curwin
>>> defined at startlf.c:236 (locfit/startlf.c:236)
>>> startlf.o:(curwin) in archive libcufflinks.a
>>> defined at c_plot.c:12 (locfit/c_plot.c:12)
>>> c_plot.o:(.bss+0x0) in archive libcufflinks.a
c++: error: linker command failed with exit code 1 (use -v to see invocation)
gmake[3]: *** [Makefile:804: cufflinks] Error 1
gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/cufflinks/work/cufflinks-2.2.1-89-gdc3b0cb/src'
gmake[2]: *** [Makefile:402: all-recursive] Error 1
gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/cufflinks/work/cufflinks-2.2.1-89-gdc3b0cb'
gmake[1]: *** [Makefile:343: all] Error 2
gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/cufflinks/work/cufflinks-2.2.1-89-gdc3b0cb'
*** Error code 1
Stop.
make: stopped in /usr/ports/biology/cufflinks
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